Báo cáo khoa học: Phosphorylation of the arginine/serine dipeptide-rich motif of the severe acute respiratory syndrome coronavirus nucleocapsid protein modulates its multimerization, translation inhibitory activity and cellular localization pptx

Phosphorylation of the arginine/serine dipeptide-rich motif
of the severe acute respiratory syndrome coronavirus
nucleocapsid protein modulates its multimerization,
translation inhibitory activity and cellular localization
Tsui-Yi Peng
1,2
, Kuan-Rong Lee
2
and Woan-Yuh Tarn
1
1 Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
2 Institute of Molecular Medicine, National Tsing Hua University, Hsin-Chu, Taiwan
An outbreak of severe acute respiratory syndrome
(SARS) occurred primarily in Asia in 2003. The causa-
tive agent of SARS is a coronavirus-related virus [1,2].
The genome sequence of the SARS virus is only mod-
erately similar to that of other species of coronaviruses
[3] and, thus, the SARS virus represents a distinct
member of the coronaviruses.
Coronaviruses are enveloped viruses with positive-
stranded, capped and polyadenylated RNA genomes
of approximately 30 kb [3,4]. The 5¢ two-thirds of the
genome encode the replicase-transcription complex
[3,4]. During viral replication, a nested set of subge-
nomic mRNAs encoding structural proteins including
the nucleocapsid (N) is synthesized via a discontinuous
transcription mechanism [5,6]. The N protein is the
most abundant viral protein produced throughout viral
infection and may exert several distinct functions [7].
The N protein is primarily involved in encapsidation
Keywords

coronavirus; nucleocapsid protein;
phosphorylation; RS domain; stress granules
Correspondence
W Y. Tarn, Institute of Biomedical
Sciences, Academia Sinica, 128 Academy
Road, Section 2, Nankang, Taipei 11529,
Taiwan
Fax: +886 2 2782 9142
Tel: +886 2 2652 3052
E-mail:
(Received 15 April 2008, revised 17 June
2008, accepted 19 June 2008)
doi:10.1111/j.1742-4658.2008.06564.x
Coronavirus nucleocapsid protein is abundant in infected cells and partici-
pates in viral RNA replication and transcription. The central domain of
the nucleocapsid protein contains several arginine ⁄ serine (RS) dipeptides,
the biological significance of which has not been well investigated. In the
present study, we demonstrate that the severe acute respiratory syndrome
coronavirus nucleocapsid protein is phosphorylated primarily within the
RS-rich region in cells and by SR protein kinase 1 in vitro. The nucleo-
capsid protein could suppress translation and its RS motif is essential
for such an activity. Moreover, phosphorylation of the RS motif could
modulate the translation inhibitory activity of the nucleocapsid protein.
We further found that RS motif phosphorylation did not significantly
affect RNA binding of the nucleocapsid protein but impaired its multimer-
ization ability. We observed that the nucleocapsid protein could translocate
to cytoplasmic stress granules in response to cellular stress. Deletion or
mutations of the RS motif enhanced stress granule localization of the
nucleocapsid protein, whereas overexpression of SR protein kinase 1 inhi-
bited nucleocapsid protein localization to stress granules. The nucleocapsid

protein lacking the RS motif formed high-order RNP complexes, which
may also account for its enhanced stress granule localization. Taken
together, phosphorylation of the severe acute respiratory syndrome-CoV
nucleocapsid protein modulates its activity in translation control and also
interferes with its oligomerization and aggregation in stress granules.
Abbreviations
GST, glutathione S-transferase; HBV, hepatitis B virus; MHV, mouse hepatitis virus; N, nucleocapsid; NDRS, RS-deleted mutant; PABP1,
poly(A)-binding protein 1; RS, arginine ⁄ serine; SARS, severe acute respiratory syndrome; SG, stress granule; SRPK, SR protein kinase.
4152 FEBS Journal 275 (2008) 4152–4163 ª 2008 The Authors Journal compilation ª 2008 FEBS
and packaging of viral genomic RNA [8–10]. More-
over, it binds to the 5¢ and ⁄ or 3¢ end of the genomic
RNA [11–13] and may participate in viral genome rep-
lication and subgenomic mRNA transcription [14,15].
However, other evidence suggests that the N protein is
dispensable for these processes [16]. In addition, the
mouse hepatitis virus (MHV) N protein stimulates
translation of a reporter mRNA containing an intact
MHV 5¢-untranslated region, probably by binding to a
tandem repeat of UCYAA in the leader sequence [17].
By contrast, recent evidence indicates that the SARS-
CoV N protein interferes with translation through its
interaction with cellular translation elongation factor
1a [18]. In addition, the SARS-CoV N protein can
inhibit the activity of cellular cyclin-dependent kinases
and thereby perturb S phase progression of virus-
infected cells [19,20]. Therefore, coronavirus N proteins
may affect various cellular functions.
Within various coronaviruses, the N protein varies
from 377 to 455 amino acid residues in length.
Although the sequence conservation between N pro-

teins is relatively low [3,21], they are likely to adopt a
common secondary structure essentially consisting of
two functional domains. The N-terminal domain inter-
acts with RNA through a structural module rich in
positively charged residues [22–24]. The RNA binding
capacity of the N protein is critical for viral infectivity
[24]. The C-terminal domain folds into a b-sheet plat-
form engaged in homodimerization [24,25] and may
also confer the RNA binding activity [10]. Moreover,
RNA binding may promote multimerization of the N
protein, implicating a nucleocapsid formation mecha-
nism [10,23,26].
Between the two functional domains is a structurally
flexible segment containing several arginine ⁄ serine
(RS)-dipeptides. This RS-rich motif is characteristic of
cellular precursor mRNA (pre-mRNA) splicing fac-
tors, termed SR proteins [27]. The RS domain is
dynamically phosphorylated by several SR protein
specific kinases, such as those of the SR protein kinase
(SRPK) and Clk families [28]. Phosphorylation of the
RS domain modulates the activity, protein–protein
interactions and subcellular localization of SR proteins
[29]. Coronavirus N proteins are phosphorylated in
host cells and in virions [25,30,31] and it has been
reported that phosphorylation affects the RNA bind-
ing specificity and nucleocytoplasmic shuttling of the
N proteins [25,32]. Indeed phosphorylation can occur
within the RS motif of coronavirus N proteins [19,33]
and this motif may play a role in C-terminal domain
dimerization [26]. Nevertheless, whether phosphoryla-

tion of the RS motif can modulate the functions of N
proteins remains to be examined in detail.
Coronavirus N proteins localize to both the cyto-
plasm and the nucleolus in virus-infected cells [34–36]
and can shuttle between the nucleus and the cytoplasm
[37]. Nucleolar localization of N protein requires
regions in the protein that are rich in arginine residues
and is likely cell cycle-dependent [20,35,36]. The avian
infectious bronchitis virus N protein indeed interacts
with and colocalizes with the nucleolar proteins nucle-
olin and fibrillarin [38,39]. However, the ability of
nucleolar localization varies between N proteins of
different coronaviruses [36]. The SARS-CoV N protein
is poorly localized to the nucleolus [36]. In the present
study, we found that the SARS-CoV N protein
appeared in cytoplasmic stress granules (SGs). When
eukaryotic cells encounter environmental stress,
mRNA metabolism is reprogrammed to adapt to
stress-induced damage. Translationally stalled mRNAs
together with a number of translation initiation factors
and RNA-binding proteins are deposited into SGs
[40]. Formation of SGs can also be induced by over-
expression of the prion-like RNA binding protein
TIA-1 [41]. Upon stress induction, TIA-1 forms aggre-
gates in SGs and may play a role in translation inhibi-
tion [41].
In the present study, we examined phosphorylation
of the SARS-CoV N protein. Our data provide
evidence that phosphorylation of the N protein pri-
marily occurs within its RS-rich motif and may affect

its oligomerization, translation inhibitory activity and
subcellular localization.
Results
Phosphorylation of the RS-rich motif of the
SARS-CoV N protein
Coronavirus N proteins are phosphoproteins [30,32].
The N protein of all coronaviruses, including the
SARS-CoV, contains an RS-rich motif (Fig. 1) that
likely provides potential phosphorylation sites for
multiple cellular kinases [32]. We predicted that N
proteins, due to their similarity with cellular SR proteins
in the RS-rich motif, may serve as a substrate of SR
protein specific kinases. To study phosphorylation of
SARS-CoV N protein RS domain, we overexpressed
FLAG-tagged N protein and the RS-deleted mutant
(NDRS) in HEK293 cells. Transfected cells were incu-
bated with [
32
P]orthophosphate for labeling. Anti-
FLAG immunoprecipitation of the full-length N
protein from the cell lysate revealed a
32
P-labeled band
at approximately 52 kDa (Fig. 2A, lane 1), similar
to previous reports [42], indicating that the SARS-CoV
N protein was phosphorylated in vivo. However,
T Y. Peng et al. Phosphorylation of SARS CoV-N protein RS motif
FEBS Journal 275 (2008) 4152–4163 ª 2008 The Authors Journal compilation ª 2008 FEBS 4153
inefficient labeling of NDRS (Fig. 2A, lane 2) suggested
that the RS motif is the major phosphorylation site for

the SARS-CoV N protein in cells. We next examined
whether the SR protein kinase SRPK1 can phos-
phorylate the N protein within its RS-rich motif.
Full-length N and NDRS were each fused to glutathione
Fig. 1. Schematic representation of the domain structure of the SARS-CoV N protein and RS-rich motif sequence alignment of the coronavi-
rus N proteins. Functional motifs and domains are depicted as previously described. Alignment of the RS-rich motifs was performed using
CLUSTALW of the European Molecular Biology Laboratory’s European Bioinformatics Institute (Hinxton, UK). The arginine and serine residues
of the RS motif are highlighted in gray. The accession number of the indicated coronavirus N proteins is: feline coronavirus (FCoV;
BAC01161), porcine respiratory coronavirus (PRC; CAA80841), mouse MHV (P03416), human SARS coronavirus (AAP37024) and avian infec-
tious bronchitis virus (AAA46214). Bottom: serine-to-alanine mutants of the SARS-CoV N protein that were used in the study.
AB C
D
Fig. 2. Phosphorylation of the SARS-CoV N protein within the RS-rich motif. (A) HEK293 cells that transiently expressed FLAG-tagged full-
length N protein (lane 1) or NDRS (lane 2) were fed [
32
P]orthophosphate. Immunoprecipitation of FLAG-tagged proteins was performed using
anti-FLAG; full-length N protein is indicated by the arrow. Lane 3 shows mock-transfection. The lower panel shows anti-SARS-CoV N immu-
noblotting. (B) Recombinant GST and GST-N (wild-type and DRS) proteins (lower: Coomassie blue staining) were phosphorylated by purified
SRPK1 in reactions containing [c-
32
P]ATP (upper: autoradiography). (C) The CD spectrum of purified GST-NDRS was monitored in the range
190–250 nm. The y-coordinate shows De. (D) Wild-type and mutant GST-N proteins and GST-NDRS were in vitro phosphorylated by SRPK1
as in (B) (upper: autoradiography; lower: Coomassie blue staining). Values below the gel represent relative phosphorylation levels; the data
were obtained from two to three independent experiments.
Phosphorylation of SARS CoV-N protein RS motif T Y. Peng et al.
4154 FEBS Journal 275 (2008) 4152–4163 ª 2008 The Authors Journal compilation ª 2008 FEBS
S-transferase (GST) and subjected to in vitro phos-
phorylation using purified SRPK1. Figure 2B shows
that only full-length N protein was phosphorylated by
SRPK1. However, neither another SR protein kinase,

Clk1, nor protein kinase A was able to phosphorylate
the N protein in vitro (see supplementary Fig. S1). To
avoid the possibility that inefficient phosphorylation of
NDRS resulted from its improper folding, recombinant
GST-NDRS protein was analyzed by CD spectroscopy.
The CD spectrum of purified NDRS suggested that this
truncated protein still adopted an ordered conforma-
tion (Fig. 2C) and was also similar to that of the
full-length N protein (data not shown). Taken together,
these data suggest that the RS-rich region of the SARS-
CoV N protein is possibly phosphorylated by SRPK1.
Phosphorylation of multiple serines within the
RS motif
The RS motif of the SARS-CoV N protein is divergent
from that of canonical SR proteins and contains fewer
RS dipeptides. To determine which serines might be
the major phosphorylation sites, we made a series of
serine to alanine substitution mutants and investigated
their phosphorylation using SRPK1. As shown in
Fig. 2D, increasing the number of alanine substitution
gradually decreased the phosphorylation level of the N
protein. This result indicated that multiple serines are
phosphorylated, and was consistent with the observa-
tions made for other SR proteins [43]. However,
because N-8A was much poorly phosphorylated
compared to N-6A (Fig. 2D, lanes 3 and 4), S
203
S
204
might serve as the primary site of SRPK1-mediated

phosphorylation.
RS motif phosphorylation modulates the activity
of the N protein in translation suppression
Previous reports indicate that MHV infection induces
host translational shut-off [44]. Coronavirus N pro-
teins are primarily distributed throughout the cyto-
plasm, with a higher concentration within nucleoli
[21,35,39] and, thus, have the potential to interfere
with ribosome biogenesis or translation in host cells.
To test whether the SARS-CoV N protein plays a role
in translation control and whether phosphorylation
modulates its activity, we performed an in vitro trans-
lation assay. Using a firefly luciferase reporter, we
titrated recombinant GST-N or GST-NDRS protein
into the reticulocyte lysate. Both the protein level and
activity of the luciferase were measured, which may
directly reflect the translation activity because lucifer-
ase mRNA levels were similar between treatments
(Fig. 3, bottom). The GST-N protein suppressed lucif-
erase translation in a dose-dependent manner but this
translation suppressive effect was attenuated upon
phosphorylation by SRPK1 (Fig. 3). GST-NDRS or
GST control had no significant effects on translation
of the luciferase mRNA. Therefore, the SARS-CoV N
protein might possess translation suppression activity
that requires its RS motif and, thus, could be modu-
lated by phosphorylation.
Effect of RS motif phosphorylation on
oligomerization of the N protein
To better understand the effect of RS motif phosphor-

ylation on the biological function of the N protein, we
Fig. 3. The translation inhibition activity of the SARS-CoV N protein
is modulated by phosphorylation. Translation of an in vitro tran-
scribed firefly luciferase mRNA was performed in reticulocyte
lysate in the presence of different amounts of nonphosphorylated
(N) or phosphorylated (pN) GST-N, GST-NDRS or GST protein.
Representative autoradiograms show the resulting firefly luciferase
protein; Coomassie blue staining shows titrated N protein (N) and
a reticulosyte lysate protein (*) as loading control. The graph shows
relative translation efficiency obtained by comparison with the reac-
tion without N protein; data are the mean ± SD values are from
three independent experiments. In vitro translation reactions con-
tained 1 lg of indicated recombinant protein as well as
32
P-labeled
luciferase reporter mRNA as tracer. After incubation, the level and
the integrity of radioisotope labeled RNA were examined on a dena-
turing 4% polyacrylamide gel.
T Y. Peng et al. Phosphorylation of SARS CoV-N protein RS motif
FEBS Journal 275 (2008) 4152–4163 ª 2008 The Authors Journal compilation ª 2008 FEBS 4155
next examined the RNA binding activity of the SARS-
CoV N protein. His-tagged N protein was used to
avoid dimerization caused by GST. Recombinant
His-N protein was subjected to in vitro phosphoryla-
tion by SRPK1. Figure 4A shows that His-N was
32
P-labeled after phosphorylation and protein phos-
phatase treatment removed
32
P phosphates (Fig. 4A,

lanes 2 and 3). Moreover, phosphorylation resulted in
AC
B
D
E
Fig. 4. Effects of RS motif phosphorylation on the RNA binding activity and multimerization of the SARS-CoV N protein. (A) Recombinant
His-tagged N protein was phosphorylated by SRPK1 (lanes 2 and 3) or mock-phosphorylated (lane 1) in the presence (upper panel) or
absence (lower panel) of [c-
32
P]ATP. Phosphorylated N protein was subsequently treated with k-protein phosphatase (lane 3) or mock-trea-
ted (lane 2). (B) An increasing amount of mock- (N) or SRPK1- (pN) phosphorylated N protein was incubated with an approximately
110 nucleotide
32
P-labeled RNA probe, and binding was analyzed by electrophoresis on a nondenaturing polyacrylamide gel. C1, C2, C3 and
C4 denote RNP complexes that may contain two, three, four and six copies of the N protein, respectively. (C) The RNA binding efficiency of
N protein is represented as a percentage of bound RNA (i.e. the percentage of bound RNA = 100%)percentage of free probe). The apparent
K
d
was calculated as ½ V
max
. Each SD was obtained from four independent experiments. (D) The relative abundance (percentage) of
unbound RNA and distinct RNA ⁄ N protein complexes was calculated as 100 · (arbitrary unit of each band in individual lane divided by the
unit of the unbound RNA detected in the absence of the N protein). The results are representative of four independent experiments. (E)
Chemical crosslinking of nonphosphorylated (N) and phosphorylated (pN) N proteins (lanes 2 and 4). Lanes 1 and 3 are the mock reactions
without crosslinker. The right-hand panel shows the relative abundance (percentage) of monomer and crosslinked forms. Percentage was
calculated as 100 · (arbitrary unit of each form divided by the sum units of all forms).
Phosphorylation of SARS CoV-N protein RS motif T Y. Peng et al.
4156 FEBS Journal 275 (2008) 4152–4163 ª 2008 The Authors Journal compilation ª 2008 FEBS
slight mobility shift of the N protein (lane 2), possibly
indicating its stoichiometric phosphorylation. Next,

electrophoretic mobility shift assay showed that non-
phosphorylated His-N bound an approximately
110 nucleotide RNA probe with an apparent dissocia-
tion constant of 52.9 nm, comparable to that reported
previously [45,46]. Moreover, His-N appeared to form
oligomers in a concentration-dependent manner
(Fig. 4B,C). The phosphorylated N protein also bound
this RNA probe and its dissociation constant was
determined to be 66.7 nm, which was similar to that of
nonphosphorylated N protein (Fig. 4C). However, for-
mation of high-order N protein RNP complexes
appeared to be impaired when the N protein was phos-
phorylated (Fig. 4D). Chemical crosslinking of the N
protein confirmed that phosphorylated N was less
capable of forming oligomers than the nonphosphory-
lated one (Fig. 4E). Therefore, it is likely that phos-
phorylation of the RS motif interferes with
oligomerization of the N protein.
Translocation of the N protein to stress granules
is modulated by RS motif phosphorylation
Because the RS domain can modulate subcellular
localization of cellular SR proteins [45], we next exam-
ined whether the RS motif of SARS-CoV N protein
has this activity. When the FLAG-tagged NDRS
fusion protein was transiently expressed in HeLa cells,
approximately 5% of transfected cells showed a punc-
tate staining pattern (Fig. 5A). This granule-like locali-
zation pattern was also observed with the full-length N
protein, albeit rarely (approximately 1% of the trans-
fected cells). Although this granule staining pattern

was observed only in a few percent of N or NDRS-
protein expressing cells under normal cell conditions, it
was greatly enhanced upon arsenite treatment (> 95%
transfected cells; Fig. 5B). Indeed both N and NDRS
colocalized with endogenous poly(A)-binding protein 1
(PABP1) and transiently expressed TIA-1 (Fig. 5B),
both of which are SG components [40].
To distinguish whether the RS motif deletion or a
lack of phosphorylation enhanced N protein localiza-
tion in SGs, we examined the cellular localization of
two RS motif mutants, N-6A and N-14A. Both
mutants showed a higher tendency towards SG locali-
zation than the wild-type N (Fig. 5A), suggesting that
SG localization of the N protein primarily resulted
from its hypophosphorylation. Moreover, the N-termi-
nal (N
NT
) but not the C-terminal (N
CT
) part of the N
protein appeared to be responsible for granule localiza-
tion (Fig. 5A). We apparently reasoned that the N-ter-
minal domain contains the RS motif and confers RNA
A
B
Fig. 5. Translocation of the SARS-CoV N protein to cytoplasmic
granules can be induced by cell stress and modulated by phosphor-
ylation. (A) Expression vector encoding FLAG-tagged full-length (N),
RS motif-deleted (NDRS), two serine-to-alanine mutants (N-6A and
N-14A), N-terminal-half (N

NT
) or C-terminal-half (N
CT
) N protein was
transiently transfected into HeLa cells. Upper panel: representative
fluorescence images. Lower panel: percentage of granule-positive
cells; approximately 100 transfected cells were counted for each
protein. (B) HeLa cells transiently expressing HA-tagged N or NDRS
or coexpressing HA-N and GFP-TIA-1 were mock treated ())or
treated (+) with 0.5 m
M arsenite for 1 h. Double immunofluores-
cence was performed using anti-HA and anti-PABP. A merged
image is shown in the right-hand panel.
T Y. Peng et al. Phosphorylation of SARS CoV-N protein RS motif
FEBS Journal 275 (2008) 4152–4163 ª 2008 The Authors Journal compilation ª 2008 FEBS 4157
binding ability [10,22] and is therefore capable of
forming granules. Next, we evaluated SRPK1-mediated
RS motif phosphorylation in modulating SG localiza-
tion or retention of the N protein. FLAG-tagged N
protein and HA-tagged SRPK1 were transiently coex-
pressed in HeLa cells. In the presence of overexpressed
SRPK1, the N protein was unable to localize to SGs,
even after arsenite treatment of the cells (Fig. 6, white
arrows). However, SRPK1 overexpression could not
disperse RS deletion or alanine substitution mutants to
the cytoplasm (NDRS and N-14A; Fig. 6). Under this
condition, PABP1, similar to NDRS and N-14A,
showed a granular pattern (Fig. 6, lower panel), indi-
cating that SG assembly is not disturbed by overex-
pression of SRPK1. Therefore, phosphorylation of the

RS motif might diminish N protein oligomerization
(Fig. 4) and thereby prevent its aggregation in SGs.
Together, the SARS-CoV N protein could target to
SGs, reflecting its role in translation suppression.
Moreover, phosphorylation of the RS motif modulates
the ability of the N protein to form SGs.
RS motif deletion induces the N protein to form
large RNP complexes
The SARS-CoV N protein might regulate translation
and could target to SGs; therefore, we evaluated
whether it forms RNPs in host cells. Using glycerol
gradient sedimentation, we observed that the N protein
formed RNPs in cells because it was moved to lighter
density fractions after RNase treatment (Fig. 7A).
Compared to full-length N, NDRS even migrated in
heavier fractions of the sucrose density gradient
(Fig. 7B). The high-order NDRS complexes were also
sensitive to RNase (data not shown). Therefore,
removal of the RS motif from the N protein induced
larger RNP formation, which may account for NDRS
aggregation in SGs. The above data show that RS
motif deletion induced high-order N protein-containing
RNP formation. We inferred that this might result
from hypophosphorylation of the NDRS protein.
Discussion
The RS domain is a characteristic feature of cellular
pre-mRNA splicing factors [27,29]. Several viral pro-
teins also contain various numbers of repeated RS
dipeptides. The transactivator E2 protein of cutaneous
papillomaviruses has a relatively long RS domain,

which functions to recruit cellular splicing factors for
Fig. 6. Overexpression of SRPK1 prevents N protein translocation
to stress granules. HeLa cells were transiently cotransfected with
vectors encoding FLAG-tagged full-length N, N-14A or NDRS and
HA-tagged SRPK1, and treated with arsenite as in Fig. 4B. Immuno-
fluorescence using anti-HA and anti-FLAG was performed; two rep-
resentative images are shown for the N protein. Arrowheads
indicate cells that expressed FLAG-N protein alone, and white
arrows indicate cells expressing both FLAG-N and HA-SRPK1. Cell
nuclei were stained with 4¢,6¢-diamidino-2-phenylindole (DAPI). The
lower panel shows double immunofluorescence of HA-SRPK1-over-
expressing HeLa cells using anti-HA and anti-PABP. Yellow arrows
indicate cells that overexpressed HA-SRPK1.
A
B
Fig. 7. The SARS-CoV N protein forms RNPs in cell. (A) Mock- or
RNase-treated HEK293 cell lysate containing HA-tagged N protein
was fractionated on a 10–30% glycerol density gradient. (B) Lysate
containing full-length N or NDRS protein was fractionated on a
10–30% sucrose density gradient. N protein was detected by
immunoblotting with anti-SARS-CoV N serum.
Phosphorylation of SARS CoV-N protein RS motif T Y. Peng et al.
4158 FEBS Journal 275 (2008) 4152–4163 ª 2008 The Authors Journal compilation ª 2008 FEBS
cotranscriptional splicing regulation [47]. The core
protein of hepatitis B virus (HBV) has an arginine-rich
domain at the C-terminus that bears a few RS dipep-
tides. The HBV core protein can be phosphorylated by
SRPK1 and SRPK2 [48]. Similar to the HBV core,
coronavirus N proteins contain a short RS-rich motif
(Fig. 1) and the SARS-CoV N protein might be phos-

phorylated by SRPK1 (Fig. 2). We have examined
whether the SARS-CoV N protein plays a role in pre-
mRNA splicing due to the presence of the RS motif
but, so far, we do not have any evidence to support
this hypothesis (data not shown). In the present study,
we provide evidence that the SARS-CoV N protein
could suppress translation at least in vitro (Fig. 3). The
potential role of the N protein in translation control
might correlate with its localization in the cytoplasmic
SGs (Fig. 5) and is also in line with recent reports that
coronavirus infection could cause translational shut-off
in host cells and that the SARS-CoV N protein may
execute this activity via its interact with elongation
factor 1a [18,44]. Although coronaviral N protein lar-
gely forms helical nucleocapsids with the viral RNA
genome during infection [10], how it participates in
translation control in host cells and whether it has any
substrate specificity or functions under certain cellular
conditions remain to be studied in the future.
Previous reports have suggested that the SARS-
CoV N protein can act as a substrate of various
kinases, such as cyclin-dependent kinases, glycogen
synthase kinase, creatine kinase II and mitogen-acti-
vated protein kinase [32]. Our data show that multi-
ple serine residues within the RS motif could be
in vitro phosphorylated by SRPK1 (Fig. 2). The
SARS-CoV N protein is primarily distributed in the
cytoplasm, coincident with the cellular localization of
SRPK1. Coexpression of SRPK1 could modulate
cellular localization of the N protein, suggesting that

the N protein is a substrate of SRPK1 in cells
(Fig. 6). Phosphorylation of the transmissible gastro-
enteritis virus N protein also occurs on a moderately
conserved serine within the RS motif, although which
kinases could phosphorylate this serine is as yet
unknown [33]. In the present study, we provide
evidence that SRPK1-mediated RS motif phos-
phorylation influences the biochemical and biological
activities of the SARS-CoV N protein. First, the
potential translation suppression activity of the
SARS-CoV N protein might be modulated by phos-
phorylation (Fig. 3). Moreover, phosphorylation may
also impact on its oligomerization, cellular localiza-
tion and perhaps RNP complex formation (Figs 4–7).
The questions of whether SRPK1 phosphorylates the
SARS-CoV N protein in cells particularly during viral
infection and where this phosphorylation occurs
remain to be answered.
A mammalian two-hybrid assay previously showed
that the RS motif is directly involved in N protein self-
interaction [42]. However, other evidence indicated
that the RS motif interferes with SARS-CoV N protein
multimerization but this activity requires its C-terminal
domain [26]. Our data show that RS motif phosphory-
lation partially impaired N protein multimerization
(Fig. 4). Perhaps such phosphorylation modulates the
balance between N protein self-association and dissoci-
ation, which thereby impacts on its cellular functions.
Multimerization of the N protein is necessary for
nucleocapsid formation and assembly of the viral

particles [42]. Thus, whether phosphorylation of the
RS motif in virions could modulate N protein function
in encapsulation of genomic RNA remains to be inves-
tigated. Moreover, we observed that deletion of the RS
motif greatly enhanced association of the SARS-CoV
N protein with cellular RNPs (Fig. 7). Perhaps RS
motif phosphorylation prevents nonspecific binding of
the N protein to cellular RNP complexes and thus aids
viral genome packaging into capsids; this possibility
also remains to be tested.
During infection, coronaviral N protein participates
in virus replication that probably occurs at the sites
associated with ER-derived membrane tubules and
vesicles [49]. Subsequently, viral nucleocapsids are
transported to the budding sites in the Golgi region
for viral particle formation. Although overexpressed,
most coronavirus N proteins are located in the cyto-
plasm as well as in the nucleolus [34,35]. Nevertheless,
the SARS-CoV N protein does not localize substan-
tially to the nucleolus [36,50], as also observed in the
present study (Fig. 5). It has been proposed that
the signals for nuclear and nucleolar targeting of the
SARS-CoV N protein are poorly accessible to the
nuclear import machinery due to phosphorylation
regulation or conformational constrains [36,50]. Never-
theless, the present study has revealed for the first
time that overexpressed SARS-CoV N protein might
localize to SGs in HeLa cells (Fig. 5). Such an SG
localization pattern was enhanced by deletion or phos-
phorylation site mutations of the RS motif and was

obvious in stress-treated cells (Fig. 5). SGs contain
mRNPs whose translation is temporarily blocked [40].
Therefore, the N protein may sequester cellular
mRNPs in SGs and inhibit their translation, possibly
during viral infection. Nevertheless, the evidence
demonstrating that RS motif phosphorylation reduced
oligomerization of the N protein and prevented its
aggregation in SGs is likely to be in accordance with
the attenuation of its translation suppression activity.
T Y. Peng et al. Phosphorylation of SARS CoV-N protein RS motif
FEBS Journal 275 (2008) 4152–4163 ª 2008 The Authors Journal compilation ª 2008 FEBS 4159
Experimental procedures
Plasmid construction
The cDNA encoding the SARS-CoV N protein was kindly
provided by K. Peck (Academia Sinica, Taipei, Taiwan).
We generated the NDRS cDNA by ligating the PCR frag-
ments encoding amino acid residues 1–175 and 215–422,
respectively. The full-length N and NDRS cDNAs were each
cloned into pcDNA3 (Invitrogen, Carlsbad, CA, USA)
in-frame with the FLAG-epitope tag, and also into pCEP4
(Invitrogen) to generate the HA-tagged proteins. All the N
protein mutants were generated from the FLAG-N con-
struct using the QuikChange site-directed mutagenesis sys-
tem (Stratagene, La Jolla, CA, USA); the sequences of these
mutants were verified. The cDNAs encoding the N-terminal
(residues 1–214) and C-terminal (residues 215–422) domain
of the N protein and N-6A and N-14A were individually
cloned into pCDNA3 (Invitrogen) in-frame fusion with the
pre-engineered FLAG-tag. The pET11D-His-N vector was
obtained from T. H. Huang (Institute of Biomedical Sci-

ences, Academia Sinica) and used for production of the His-
tagged full-length N protein in Escherichia coli. The NDRS
cDNA was appropriately cloned into pET15b (Novagen,
Madison, WI, USA) for production of recombinant NDRS.
The wild-type and mutant N and NDRS cDNAs were subcl-
oned into pGEX-5X (GE Healthcare, Piscataway, NJ,
USA) using EcoRI and SalI sites to generate the GST-
fusion proteins. Subsequently, the cDNAs encoding mutant
N proteins were cloned into pGEX-5X. The pET15b-FLAG
used for in vitro transcription of an RNA probe was con-
structed by insertion of the FLAG-epitope coding sequence
into NheI and BamHI. The in vitro translation reporter
pFL-SV40 was constructed by replacing the renilla lucifer-
ase of pRL-SV40 (Promega, Madison, WI, USA) with the
firefly luciferase.
Cell culture, transfection and indirect
immunofluorescence
HeLa and HEK293 cells were grown in DMEM (Gibco,
Grand Island, NY, USA) supplemented with 10% fetal calf
serum and penicillin ⁄ streptomycin. Transfection was per-
formed using Lipofectamine 2000 (Invitrogen) as recom-
mended by the manufacturer. For stress treatment, HeLa
cells were cultured in the presence of 0.5 mm arsenite for
1 h. The procedure for indirect immunofluorescence was
essentially as described previously [47]. Polyclonal antibody
against the HA epitope was from BAbCO (Richmond, CA,
USA). Monoclonal anti-FLAG and anti-PABP were from
Sigma (St Louis, MO, USA). Fluorescein isothyocyanate
and rhodamine conjugated secondary antibodies were from
Cappel Laboratories Cochranville, PA, USA. Immuno-

stained cells were visualized with an Axiovert 200 micro-
scope (Carl Zeiss Inc., Oberkochen, Germany).
Recombinant proteins
The His-tagged SARS-CoV N and NDRS proteins were
overproduced in E. coli BL21 (DE3). The bacterial lysate
was prepared in a buffer containing 50 mm sodium phos-
phate (pH 8.0), 300 mm NaCl and 6 m urea, and was sub-
sequently passed through His•Bind Resin (Novagen) for
purification of His-tagged proteins. Bound proteins were
eluted using the above buffer containing 250 mm imidazole.
The eluate was dialyzed against a buffer containing 50 mm
sodium phosphate (pH 7.4), 100 mm NaCl, 1 mm EDTA
and 0.01% NaN
3
. GST and GST-fusion to N, NDRS and
all mutant proteins were overproduced in E. coli strain
BL21 and purified over glutathione-Sepharose beads (GE
Healthcare) as recommended by the manufacturer. Purified
GST fusion proteins were dialyzed against buffer D (20 mm
Hepes, pH 7.9, 50 mm KC1, 0.5 mm dithiothreitol, 0.2 mm
EDTA and 20% glycerol).
Phosphorylation
For in vivo phosphorylation, 3 · 10
6
transfected HeLa cells
expressing FLAG-N or NDRS in a 60 mm diameter plate
were incubated in sodium phosphate-deficient DMEM
(Invitrogen) supplemented with 0.75 mCi [
32
P]orthophos-

phate (Amersham, Little Chalfont, UK) for 2.5 h. FLAG-
tagged protein was immunoprecipitated from the cell lysates
using anti-FLAG M2 agarose (Sigma) in a buffer containing
10 mm sodium phosphate (pH 7.2), 150 mm NaCl, 2 mm
EDTA, 1% NP-40 and a mixture of protease inhibitors
(Roche, Indianapolis, IN, USA), which was used as recom-
mended by the manufacturer. In vitro phosphorylation of
the N protein using recombinant GST-SRPK1 was essen-
tially as described previously [42]; the reactions contained
5 lm ATP with or without additional 40 nm [k-
32
P]ATP.
Dephosphorylation was performed using 200 U k-protein
phosphatase (New England Biolabs, Beverly, MA, USA).
CD spectrometry
Purified recombinant GST-NDRS (3 lm)in20mm potas-
sium acetate, 5 mm sodium acetate, 2 mm magnesium
acetate and 1 mm EGTA was subjected to far-UV CD
analysis using a Jasco J-720 spectropolarimeter (Jasco Inc.,
Easton, MD, USA). The measurement was performed in the
range 190–250 nm in a 1 mm path length cuvette at room
temperature. The data were recorded at 1 nm intervals.
Electrophoretic mobility shift assay
The approximately 110 nucleotide RNA probe was in vitro
transcribed by T7 RNA polymerase using BamHI-digested
pET15b-FLAG as template. The RNA was uniformly
labeled with [a-
32
P]UTP with a specificity activity at
approximately 1.4 · 10

4
c.p.m.Æng
)1
. Recombinant His-N
Phosphorylation of SARS CoV-N protein RS motif T Y. Peng et al.
4160 FEBS Journal 275 (2008) 4152–4163 ª 2008 The Authors Journal compilation ª 2008 FEBS
protein was incubated with 5 · 10
4
c.p.m. of
32
P-labeled
RNA in a 20 lL reaction containing 10 mm Hepes
(pH 7.9), 50 lm EDTA, 10% glycerol, 1 mm dithiothreitol,
5mm MgCl
2
, 0.1 mg of BSA, 2.5 lg of tRNA and 10 U of
RNasin (Promega) at 25 °C for 15 min. Samples were frac-
tionated on a 6% polyacrylamide nondenaturing gel in 0.5·
TBE buffer (45 mm Tris–HCl, 45 mm boric acid, 1 mm
EDTA, pH 8.0). Quantification was performed using
Typhoon9410 Variable Mode Imager (Amersham).
Chemical crosslinking
The crosslinker disuccinimidyl suberate (Sigma) was pre-
pared in N,N-dimethylformamide (Sigma) and used for
chemical crosslinking of recombinant His-tagged N protein.
The reaction mixtures contained 0.35 mm phosphorylated
or nonphosphorylated N protein and 5 mm crosslinker in
the NMR buffer (5 mm Hepes, 100 mm NaCl, 2 mm KCl,
1mm MgCl
2

,2mm CaCl
2
and 0.5 mm EDTA, pH 7.8).
The reaction was performed at 4 °C for 1 h and stopped by
100 mm glycine. Proteins were fractionated by SDS ⁄ PAGE
and detected by immunoblotting using anti-SARS-CoV N
serum (Imgenex, San Diego, CA, USA). Quantification was
performed using image j software (National Institutes of
Health, Bethesda MD, USA).
In vitro translation
The TNT coupled reticulocyte lysate system (Promega) was
used for in vitro translation of a firefly luciferase reporter
mRNA that contained 68 and 42 nucleotides in the 5¢ and
3¢ UTR, respectively, and was in vitro synthesized by T7
RNA polymerase from the template pFL-SV40. Each
10 lL of translation reaction contained 100 ng of the lucif-
erase mRNA and different amounts of recombinant GST-
NorNDRS protein. The resulting luciferase activity was
assessed by the luciferase assay system (Promega). To visu-
alize luciferase protein, [
35
S]methionin was added into the
reaction according to the manufacturer’s recommendation.
Sucrose and glycerol gradient sedimentation
HEK293 cells were transiently transfected with the vector
expressing HA-tagged N or NDRS protein. The cell lysate
was then prepared in 10 mm Tris–HCl (pH 7.4), 150 mm
NaCl and 3 mm MgCl
2
for sucrose gradient or in 20 mm

Hepes (pH 7.9), 100 mm KCl and 1 mm MgCl
2
for glycerol
gradient; both buffers additionally contained 100 l g ÆmL
)1
cycloheximide, 35 lgÆmL
)1
digitonin and 20 UÆmL
)1
RNa-
sin (Promega). Density gradient sedimentation was
performed in a Beckman SW41 rotor (Beckman-Coulter,
Fullerton, CA, USA) at 4 °C; for sucrose and glycerol
gradient sedimentation, the centrifugation condition was
30 000 g for 5 h and 74 000 g for 16 h, respectively.
Proteins were precipitated by 20% trichloroacetic acid from
each fraction and analyzed by immunoblotting using anti-
SARS-CoV N serum.
Acknowledgements
We thank Tai-Huang Huang and Konan Peck for the
SARS-CoV N protein cDNAs, plasmids and recombi-
nant proteins, and Chwan-Deng Hsiao and Yi-Wei
Chang for CD analysis. We thank Ru-Inn Lin and
Wei-Lun Chang for their initial experimental assistance
and Dr Tim C. Taylor for editing the manuscript. This
work was supported by the National Science Council
of Taiwan (NSC 95-3112-B001-007).
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Supplementary material
The following supplementary material is available
online:
Fig. S1. The SARS N protein is phosphorylated by
SRPK1 but not by Clk1 and PKA.
This material is available as part of the online article
from
Please note: Blackwell Publishing is not responsible
for the content or functionality of any supplementary
materials supplied by the authors. Any queries (other
than missing material) should be directed to the corre-
sponding author for the article.
T Y. Peng et al. Phosphorylation of SARS CoV-N protein RS motif
FEBS Journal 275 (2008) 4152–4163 ª 2008 The Authors Journal compilation ª 2008 FEBS 4163